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The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins

Nature Structural & Molecular Biology volume 13, pages 436–443 (2006)Cite this article

Abstract

α-sarcin ribotoxins comprise a unique family of ribonucleases that cripple the ribosome by catalyzing endoribonucleolytic cleavage of ribosomal RNA at a specific location in the sarcin/ricin loop (SRL). The SRL structure alone is cleaved site-specifically by the ribotoxin, but the ribosomal context enhances the reaction rate by several orders of magnitude. We show that, for the α-sarcin–like ribotoxin restrictocin, this catalytic advantage arises from favorable electrostatic interactions with the ribosome. Restrictocin binds at many sites on the ribosomal surface and under certain conditions cleaves the SRL with a second-order rate constant of 1.7 × 1010 M−1 s−1, a value that matches the predicted frequency of random restrictocin-ribosome encounters. The results suggest a mechanism of target location whereby restrictocin encounters ribosomes randomly and diffuses within the ribosomal electrostatic field to the SRL. These studies show a role for electrostatics in protein-ribosome recognition.

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Figure 1: Coulomb force dominates the interaction between restrictocin and oligonucleotides.
Figure 2: Ribosomes as substrates for restrictocin.
Figure 3: Mutation of cationic surface residues of restrictocin mitigates the ribosome advantage over SRL.
Figure 4: Monitoring restrictocin activity at dilute ribosome concentrations.
Figure 5: Side view of the 2.4 Å crystal structure of the large ribosomal subunit41,42.
Figure 6: Titration of the restrictocin-binding sites on the ribosomal surface.

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Acknowledgements

We are grateful to Y.-L. Chan for valuable advice and discussion, J. Olvera for excellent technical assistance and M. Yousef for the help at the Biophysical Core Facility at the University of Chicago. We thank I.G. Wool, P.B. Moore and members of the Piccirilli laboratory for helpful comments on the manuscript. This work was supported by grants from the Burroughs Wellcome Fund to A.V.K., from the Howard Hughes Medical Institute to J.A.P. and from the US National Institutes of Health (GM59782) to C.C.C.

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Author notes

  1. Carl C Correll

    Present address: Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, 60064, USA

Authors and Affiliations

  1. Department of Chemistry, The University of Chicago, Chicago, 60637, Illinois, USA

    Alexei V Korennykh & Joseph A Piccirilli

  2. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, 60637, Illinois, USA

    Joseph A Piccirilli & Carl C Correll

  3. Howard Hughes Medical Institute, The University of Chicago, Chicago, 60637, Illinois, USA

    Alexei V Korennykh & Joseph A Piccirilli

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Correspondence to Joseph A Piccirilli or Carl C Correll.

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Supplementary information

Supplementary Fig. 1

Cleavage of the rat SRL by restrictocin (PDF 140 kb)

Supplementary Fig. 2

Inhibition of ribotoxin-mediated RNA cleavage by salt (PDF 132 kb)

Supplementary Fig. 3

Km for SRL cleavage by restrictocin equals the binding constant Kd (PDF 82 kb)

Supplementary Fig. 4

Cleavage of ribosomes and total rRNA by restrictocin (PDF 615 kb)

Supplementary Fig. 5

Kinetic characterization of the 3/D triple mutant (PDF 205 kb)

Supplementary Table 1

Effect of buffer composition on the rate of SRL cleavage by restrictocin (PDF 51 kb)

Supplementary Table 2

Sequences of the RNA and DNA oligonucleotides used (PDF 67 kb)

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Korennykh, A., Piccirilli, J. & Correll, C. The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nat Struct Mol Biol 13, 436–443 (2006). https://doi.org/10.1038/nsmb1082

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